Mantis Bug Tracker

View Issue Details Jump to Notes ] Issue History ] Print ]
IDProjectCategoryView StatusDate SubmittedLast Update
0000097Rosetta[All Projects] Bad Codingpublic2012-09-06 12:412017-08-07 20:02
Assigned Toamw579 
StatusclosedResolutionwon't fix 
PlatformOSOS Version
Product Version 
Fixed in Version 
Summary0000097: Lysine (LYS.params and derivatives) has ridiculous starting conformation; may be true for other residues as well
DescriptionInstantiating a lysine residue from the params file results in a ridiculous eclipsed structure that looks more like a 5-membered ring, where the tip of the lysine overlays the backbone. Why not change the params file to have a more reasonable set of starting torsions (a common fully extended rotamer)?
Steps To ReproduceSwitch a centroid lysine to fullatom with SwitchToResidueTypeSet without repacking, or instantiate a lysine residue from scratch (like with make_pose_from_sequence) and dump to PDB
Additional InformationI bet this will cause test changes all over the place...
TagsNo tags attached.
Application(s) Affectednot an application
Command Line Usednot related to a command line
Developer Options
Fixed in SVN Versionn/a
Attached Files

- Relationships

-  Notes
Labonte (Developer)
2012-09-09 21:48

Yeah, they are all like that. The omega values are set to 0, for example. I've been bothered by this since I first joined Rosetta. But when I brought it up at the last MiniCON, some people indicated that someone had a good reason for not changing it. I'd love to change it, if everyone agrees with the idea.
Labonte (Developer)
2013-02-26 12:44

So, can I have permission on this one too?
smlewis (Administrator)
2013-02-28 14:51
edited on: 2013-02-28 14:52

It didn't get brought up at minicon...we should take it to the list and see if we can shake loose the reason we weren't supposed to change it, so we can note it here and close as unresolvable...or alternately fix it.

smlewis (Administrator)
2013-03-07 09:26

Discussion on the list came to no consensus.

Arguments in favor of the change:
-do not knowingly place nonsense rotamers that clash with their own backbone, --this confuses new/casual users
--it's ugly
--it's wrong, in the sense of we know those rotamers cannot ever be right

Arguments against:
-Obviously bad rotamers signal that the structure hasn't been properly repacked and needs to be
--Non-obviously bad rotamers will fail to signal so clearly that something was forgotten
--New users are upset by bad rotamers but respond with packing; not-so-bad rotamers might not be noticed and might go unrepacked

I think we are on track to close this as unresolvable.

- Issue History
Date Modified Username Field Change
2012-09-06 12:41 smlewis New Issue
2012-09-09 21:48 Labonte Note Added: 0000094
2012-09-09 21:49 Labonte Assigned To => Labonte
2012-09-09 21:49 Labonte Status new => confirmed
2012-09-09 21:51 Labonte Assigned To Labonte =>
2013-02-26 12:44 Labonte Note Added: 0000144
2013-02-28 14:51 smlewis Note Added: 0000147
2013-02-28 14:52 smlewis Note Edited: 0000147 View Revisions
2013-03-07 09:26 smlewis Note Added: 0000161
2017-08-07 20:02 amw579 Fixed in SVN Version => n/a
2017-08-07 20:02 amw579 Status confirmed => closed
2017-08-07 20:02 amw579 Assigned To => amw579
2017-08-07 20:02 amw579 Resolution open => won't fix

Copyright © 2000 - 2012 MantisBT Group
Powered by Mantis Bugtracker